Dr. Jeff Denny's
B.S., Furman University, 1994
M.S., Florida State University,
Ph.D., Florida State University,
Research and Teaching Interests
For a short CV, click here.
- Mathematical molecular biophysics
- Mathematical modeling with differential equations
- Protein structure determination via solid-state NMR data
- Mathematics education
Papers & Programs
- J. K. Denny, M. B. Daniel, and F. A. Kovacs, "Computing and
Fitting SSNMR Powder Patterns with the Arithmetic-Geometric Mean and
Edge Detection", Concepts in Magnetic Resonance, 30A(1); 1-20, 2007.
The python program to find chemical shift principal values using the
and edge detection heuristic algorithm can be found here.
- J. K. Denny and C. K. Trivett, "Cooling the Macon Volunteer
Clinic", The UMAP Journal, 27(4): 431-447, 2006.
The model in Berkeley Madonna
can be found here
and in XPPAUT
code can be found here.
Websites for Differential Equations & Modeling Software
- Berkeley Madonna
(not free, but you can run the demo free)
This is easy to use and solves equations quickly.
(Example file: bilogistic.mmd)
- pplane and
These run in your browser via java and are really nice. For
of 2 equations, pplane does a fantastic job with nullclines and
This is free and is often used by researchers. It is VERY powerful
and has lots of options. Of course, this means it's not as
as some of the others. It runs best in unix in my
since the Mac runs under unix now, it runs great on the Mac. You
need to have X11 installed to run it. (X11 comes free on
the DVD of
system files with the Mac.)
(Example file: seir.ode)
This is free, open source software. It is very similar to Matlab,
ode solver commands are different. It's fantastic for matrix
computations (just like Matlab is). The ode stuff runs well, and
had success with it on the Mac. It took me a little while to get
.m files working like I wanted, but now I'm happy with what I've got
(Example file: ode.m
This is a powerful piece of free, open source software for modeling and
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